Rui Wu, Dinneny Lab and Lee Chae, Rhee Lab

Complex networks of cis-regulatory elements (CREs) and their corresponding transcription factors (TFs) allow higher plants to transcriptionally control development and respond to environmental stimuli. Although in the past numerous putative CREs had been computationally predicted, only a few were experimentally verified. This has left a large gap in our understanding of what role CREs play in controlling complex tissue-specific and stress responsive transcriptional events. Here, we developed a pipeline for discovery and validation of a transcriptional network that plays a role in the salt stress response in the Arabidopsis root. The pipeline includes: bioinformatics search and functional validation of CREs using synthetic promoters, high-throughput screening of transcription factors binding the CREs via yeast-one-hybrid, and the validation of transcription factor function using gain-of-function studies. Using this pipeline, we have determined the regulatory functions of eight CREs including 6 sequences similar to known CREs. Our bioinformatic analysis has shown that CREs associated with stress responses are also highly enriched in developmentally-regulated promoters. These CREs regulate highly tissue-specific expression patterns in the root and bind transcription factors that act downstream of known stress and developmental pathways. These results suggest that developmental and stress regulatory pathways converge onto the same CREs to control expression. This study provides a new paradigm for understanding CRE function in plants and suggests that complex gene expression patterns can be controlled by single short DNA elements that act as hubs for multiple pathways.

Lee Chae

The Evolution of Plant Metabolism.

Despite our reliance on plant compounds for food, energy, shelter, and medicines, our knowledge of plant metabolism accounts for the production of less than 0.1% of the plant metabolites thought to exist in nature. To address this gap, we developed a platform that allows us to reconstruct the metabolic systems of different plant species at the genome-scale. In this talk, I'll discuss how we used the platform to perform a comparative analysis of 16 species in the green plant lineage, which shed light on how metabolic processes emerge and evolve in plants. I'll also talk about our discovery of a set of genomic signatures that provide a unique opportunity to identify previously uncharacterized genes involved in novel plant metabolic processes.